low in my opinion shouldn't be lower than the bulge of your posterior delts--lower than that and there's nothing for the bar to grab onto, and you might as well be leg pressing. i have a personal bias toward a very high bar back squat, but if you're doing a lower bar placement, really shrug the traps, squeeze the shoulder blades together and take a narrow grip instead of a wide grip--that should create some topography on your upper back to settle the bar into. again, if you're lower than that (like so low you have to take a snatch width grip), i think you're too low.
i guess my question would be why did you decide to start experimenting with such a low bar position? and if it's painful, maybe not a great idea. if you're trying to get more back work, add in some stiff-leg deadlifts or good mornings after you squat instead.